The Freedom Fighters, with new addition, Dulcy, develop a De-Roboti-sizer and try it out on Bunnie. It's a success and, against Sally's wishes, Sonic battles Robotnik's newest weapon - a Virtual Reality Shriek-Bot - and impulsively brings Uncle Chuck back to Knothole to de-roboti-size him.

The Freedom Fighters run into a Swashbuckler, named Ari, battling Swat-Bots. Sonic diverts them, allowing Ari to escape. After hearing that Robotnik is holding his band of Freedom Fighters hostage, Ari decides to help Sonic free them

Sonic attempts a solo rescue to prevent prisoners from being roboti-sized and is hit by a Memory Scrambler that erases short-term memory. Snively finds Sonic and brainwashes him into believing they are friends and that the Freedom Fighters are a subversive group which he infiltrated on Snively's behalf.

After a disastrous failed mission, Sonic laments that they can't go back and prevent Robotnik's take-over. Dulcy tells them they can and takes Sonic and Sally to the Floating Island where they find the "Time Stones", but in order to time travel to a desired destination/time, they have to synchronize their thoughts and Sonic allows his to drift (to thoughts of chili dogs). They arrive on the eve of the take-over, just in time to see a pristine Mobius and meet Uncle Chuck and their younger selves, but not in time to stop Robotnik (then called Julian) from overthrowing the King.

In Part II, Sonic and Sally steal the Roboti-sizer plans, stop the Destroyer from polluting the Great Forest and save Little Sonic, Little Sally and Dulcy's mother, Sabina, but are unable to prevent Robotnik from roboti-sizing Uncle Chuck or from relegating the King to the Void. After they return to the present, Sonic laments that the trip was a waste, but Sally reminds him that they came close and they will keep trying until they do triumph over Robotnik.

Antoine decides to study martial arts but after he wrecks most of Knothole Sonic sends him off to practice in the woods, where he runs into a scurvy band of Road Warrior-types, called the Nasty Hyenas...

After Dulcy exhibits strange behavior, Sally discovers she's going through a "rites of passage" stage of her adolescence. In Dragon tradition, she is drawn to Dragon Lair, a migratory nesting ground, through trance-like visits from her mother. Unfortunately, Robotnik, who is determined to capture all the remaining Dragons, taps into the same information. He captures a Dragon, but it isn't Dulcy. His Dragon has just laid an egg that may hatch at anytime, so the Freedom Fighters are under the gun to rescue the Mother Dragon before Robotnik can roboti-size her, then get her back to Knothole before her egg hatches.

When a blizzard hits Knothole causing Dulcy to demolish a few huts during a landing, Sonic is forced to bunk with Antoine. It is truly a marriage of opposites, with Antoine constantly picking up after Sonic. Finally, after making a complete mess of the kitchen fixing chili dogs, Sonic retires for the night. A few hours later, an exhausted Antoine follows, but almost immediately, he awakens to see Sonic "sleep-racing", leaving behind a trail of destruction. Antoine snaps and, giggling maniacally, goes on a rampage. When the other Freedom Fighters investigate the noise, they find Sonic on his way out to rebuild his hut. He can't take another night with the lunatic Antoine.

On a mission to contact the first Freedom Fighters on the King's List, Sonic and the others are forced to travel through a tunnel which carries a "curse" against all intruders. They encounter the WOLF PACK (which turns out to be the Freedom Fighters on the List) and their female leader, LUPE, who are trying to prevent the destruction of their land by a prototype POD from Robotnik's "DOOMSDAY PROJECT"...

After Antoine saves Sally's life during a raid, Sonic can't stand his bragging and zips in to see Uncle Chuck, who finds out his "bug" in Robotnik's HQ is malfunctioning. While Chuck goes to fix it, Sally and Bunnie, flying a "Rotor-created" Hover-Unit, find the Doomsday Machine and download its schematics, along with a Top Secret file detailing a plan to catch a spy by damaging the "bug" at HQ. They send back a Rocket Dove with a warning and Antoine goes to warn Chuck. When Sonic returns to Knothole and finds out what happened, he takes off but it's too late. Antoine has been captured by Snively, who decides to torture him with bad food preparation. Sonic rescues Antoine, but then Chuck is captured, after they uncover his hide-out. Sonic rescues Chuck and demands that he return to Knothole, now that his cover is blown, but Chuck shows him his new hide-out and new m. o. working in disguise.

When a Pod lands in Knothole, Sonic and Sally realize the Doomsday Machine is already in operation. The Freedom Fighter groups break into the Doomsday Machine, only to find Robotnik let them in. Sonic tries to destroy the control room but is thwarted and almost roboti-sized, then escapes using multiple Power Rings. Uncle Chuck suggests they use the Power Stones to overcome Robotnik and, with Nicole's help,, Sonic finds Robotnik's Power Stone and he and Sally sneak back inside the Doomsday Machine, where they decide to combine them as an immeasurable power source. As they streak through the Machine, Robotnik realizes. it's all over and jumps into an escape pod, while Snively escapes via a hidden elevator. But as the incredible energy source vaporizes the Machine, it overtakes Robotnik's pod. That night, as the Freedom Fighters celebrate their supreme victory over Robotnik, Snively, now on his own, decides it's his turn to rule.